Chromosome-length genome assembly of the critically endangered Mountain bongo (Tragelaphus eurycerus isaaci): a...

The Mountain bongo (Tragelaphus eurycerus isaaci), a critically endangered tragelaphine antelope native to the montane forests of Kenya, faces significant threats from habitat loss and hunting. Although the Mountain bongo is a flagship species in Kenya, the majority are found in small, isolated populations of less than 100 animals total, making it a species of high conservation concern. In this report, we present a chromosome-length draft genome assembly for the Mountain bongo, generated using a combination of linked-read and proximity ligation (Hi-C) sequencing techniques. The assembly resulted in a 2.96 Gb sized genome with a contig N50 of 79.5 kb and a scaffold N50 of 192 Mb. Assembly completeness was 95.1% based on 12,234 Benchmarking Universal Single-Copy Orthologs (BUSCO) and annotation revealed 29,820 protein-coding genes, of which 27,761 were functionally annotated, and a repetitive content of 47.31%. Synteny analysis against the domestic cattle (Bos taurus) genome assembly revealed numerous chromosomal rearrangements between the 2 species. Our analysis also revealed insights into the evolutionary and demographic history of the Mountain bongo, offering valuable information for conservation management. We also assembled and annotated the mitochondrial genome which showed <1% differences from the Lowland bongo subspecies, T. e. eurycerus. By integrating genomic data with traditional conservation methods, this reference lays the foundation to evaluate and preserve genetic diversity of both in situ and ex situ populations of the Mountain bongo amidst growing environmental pressures.